Identification and Phylogenetic Characterization of a New Subfamily of α-Amylase Enzymes from Marine Microorganisms

Marine Biotechnology

Volumn 14, Issue 3, 2012, Pages 253-260

  Liu, Yang ^a   Lei, Yin ^a   Zhang, Xuecheng ^a   Gao, Yi ^a   Xiao, Yazhong ^a   Peng, Hui ^a  

^a ANHUI UNIVERSITY   (China)

Author keywords

Amylase; Glycoside hydrolase family GH13; Metagenomic cloning; Subfamily classification

Indexed keywords

BACTERIAL GENOMES; CATALYTIC DOMAINS; GLYCOSIDASES; GLYCOSIDE HYDROLASE FAMILY GH13; GLYCOSIDE HYDROLASES; MARINE BACTERIUM; MARINE MICROORGANISM; METAGENOMIC LIBRARIES; PHYLOGENETIC CHARACTERIZATION; SEQUENCE COMPARISONS; SUBSTRATE HYDROLYSIS;

BACTERIA; ESCHERICHIA COLI; GENE ENCODING; GENETIC ENGINEERING; HYDROLYSIS;

AMYLASES;

AMYLASE; BACTERIAL PROTEIN;

COLIFORM BACTERIUM; ENZYME ACTIVITY; GENE EXPRESSION; GENOME; HYDROLYSIS; IDENTIFICATION METHOD; MARINE ENVIRONMENT; MICROORGANISM; PHYLOGENETICS; PROTEIN; SUBSTRATE;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; CLASSIFICATION; ENZYME ACTIVATION; ENZYME SPECIFICITY; ENZYME STABILITY; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEA; SEDIMENT;

ALPHA-AMYLASES; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; ENZYME ACTIVATION; ENZYME STABILITY; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; SUBSTRATE SPECIFICITY; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84859423171     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-011-9414-3     Document Type: Article

References (29)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
3. Ballschmiter M, Fütterer O, Liebl W (2006) Identification and characterization of a novel intracellular alkaline α-amylase from the hyperthermophilic bacterium Thermotoga maritima MSB8. Appl Environ Microbiol 72: 2206-2211.
4. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The carbohydrate-active enZymes database (CAZy): an expert resource for glycogenomics. Nucl Acids Res 37: 233-238.
5. Chakraborty S, Khopadea A, Kokarea C, Mahadika K, Chopade B (2009) Isolation and characterization of novel α-amylase from marine Streptomyces sp. D1. J Mol Catal B: Enzym 58: 17-23.
6. Da Lage JL, Feller G, Janeček Š (2004) Horizontal gene transfer from Eukarya to Bacteria and domain shuffling: the α-amylase model. Cell Mol Life Sci 61: 97-109.
7. Dong G, Vieille C, Savchenko A, Zeikus JG (1997) Cloning, sequencing, and expression of the gene encoding extracellular α-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microbiol 63: 3569-3576.
8. Emori M, Takagi M, Maruo B, Yano K (1990) Molecular cloning, nucleotide sequencing, and expression of the Bacillus subtilis (natto) IAM1212 α-amylase gene, which encodes an α-amylase structurally similar to but enzymatically distinct from that of B. subtilis 2633. J Bacteriol 172: 4901-4908.
9. Gupta R, Gigras P, Mohapatra H, Goswami VK, Chauhan B (2003) Microbial α-amylases: a biotechnological perspective. Process Biochem 38: 1599-1616.
10. Hostinová E, Janeček Š, Gašperŕk J (2010) Gene sequence, bioinformatics and enzymatic characterization of α-amylase from Saccharomycopsis fibuligera KZ. Protein J 29: 355-364.
11. Janeček Š, Svensson B, Henrissat B (1997) Domain evolution in the α-amylase family. J Mol Evol 45: 322-331.
12. Janeček Š, Svensson B, MacGregor EA (2007) A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31. FEBS Lett 581: 1261-1268.
13. Kennedy J, Marchesi JR, Dobson ADW (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 7: 27-34.
14. MacGregor EA, Janeček Š, Svensson B (2001) Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim Biophys Acta 1546: 1-20.
15. Machovič M, Janeček Š (2003) The invariant residues in the α-amylase family: just the catalytic triad. Biologia (Bratisl) 58: 1127-1132.
16. Malhotra R, Noorvez SM, Satyanarayana T (2000) Production and partial characterization of thermostable and calcium independent α-amylase of an extreme thermophile Bacillus thermooleovorans NP54. Lett Appl Microbiol 31: 378-384.
17. Marchler-Bauer A, Anderson JB, Cherukuri PF, De Weese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res 25: D192-D196.
18. Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 32: 426-428.
19. Najafi MF, Kembhavi A (2005) One step purification and characterization of an extracellular α-amylase from marine Vibrio sp. Enzyme Microb Tech 36: 535-539.
20. Ohdan K, Kuriki T, Kaneko H, Shimada J, Takada T, Fujimoto Z, Mizuno H, Okada S (1999) Characteristics of two forms of α-amylases and structural implication. Appl Environ Microbiol 65: 4652-4658.
21. Page RDM (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
22. Pandey A, Nigam P, Soccol CR, Soccol VT, Singh D, Mohan R (2000) Advances in microbial amylases. Appl Biochem 31: 135-152.
23. Sabathé F, Croux C, Cornillot E, Soucaille P (2002) amyP, a reporter gene to study strain degeneration in Clostridium acetobutylicum ATCC 824. FEMS Microbiol Lett 210: 93-98.
24. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
25. Stam MR, Danchin EGJ, Rancurel C, Coutinho PM, Henrissat B (2006) Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Eng Des Sel 19: 555-562.
26. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
27. van der Kaaij RM, Janeček Š, van der Maarel MJEC, Dijkhuizen L (2007) Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal α-amylase enzymes. Microbiol 153: 4003-4015.
28. Yun J, Kang S, Park S, Yoon H, Kim MJ, Heu S, Ryu S (2004) Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl Environ Microbiol 70: 7229-7235.
29. Zhang JW, Zeng RY (2008) Purification and characterization of a cold-adapted alpha-amylase produced by Nocardiopsis sp.7326 isolated from Prydz Bay, Antarctic.Mar Biotechnol 10: 75-82.